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I own 2 businesses that both use Atrex for inventory and our POS. I am combining my two businesses into 1 location and need to combine my Atrex files into one. Is there any way to do this, or do I need to re-enter all of one businesses SKU's into the other one.

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You can add the SKUs (stock codes in Atrex) from one database to the other using Options - Import - Stock Codes. The help file or user guide explains the process and the following link is to a video tutorial on importing:

PS If you do have the same stock code present in both databases, the default import mode is to update the existing stock codes. You do have the option to set the mode to import only if this is not desired.